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- PDB-8cmo: Cryo-EM structure of the Photosystem I - LHCI supercomplex from C... -

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Basic information

Entry
Database: PDB / ID: 8cmo
TitleCryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.
Components
  • (Light-harvesting protein of photosystem I ...) x 9
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 6
  • (Photosystem I subunit ...) x 2
  • Photosystem I reaction centre subunit XI PsaL
KeywordsPHOTOSYNTHESIS / Green alga / PSI / Coelastrella / membrane protein / Cryo-EM
Function / homology
Function and homology information


1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / LAURIC ACID / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / LAURIC ACID / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LPX / Chem-LUT / Chem-NKP / OCTANOIC ACID (CAPRYLIC ACID) / PHYLLOQUINONE / (3R)-beta,beta-caroten-3-ol / IRON/SULFUR CLUSTER / SPHINGOSINE / Chem-SQD / Phosphatidylinositol
Similarity search - Component
Biological speciesCoelastrella (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsFadeeva, M. / Klaiman, D. / Nelson, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation199/21 Israel
CitationJournal: To Be Published
Title: Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.
Authors: Fadeeva, M. / Klaiman, D. / Nelson, N.
History
DepositionFeb 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1 PsaA
B: Photosystem I P700 chlorophyll a apoprotein A2 PsaB
C: Photosystem I subunit VII PsaC
D: Photosystem I reaction center subunit II PsaD
E: Photosystem I reaction center subunit IV PsaE
F: Photosystem I reaction center subunit III PsaF
G: Photosystem I reaction center subunit V PsaG
I: Photosystem I reaction center subunit VIII PsaI
J: Photosystem I subunit IX PsaJ
K: Photosystem I reaction center subunit X psaK
L: Photosystem I reaction centre subunit XI PsaL
1: Light-harvesting protein of photosystem I Lhca1
Z: Light-harvesting protein of photosystem I Lhca1
3: Light-harvesting protein of photosystem I Lhca3
7: Light-harvesting protein of photosystem I Lhca7
8: Light-harvesting protein of photosystem I Lhca8
4: Light-harvesting protein of photosystem I Lhca4
5: Light-harvesting protein of photosystem I Lhca5
6: Light-harvesting protein of photosystem I Lhca6
9: Light-harvesting protein of photosystem I Lhca9
2: Light-harvesting protein of photosystem I Lhca2 partial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,389353
Polymers465,96721
Non-polymers266,421332
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 PsaA


Mass: 82115.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 PsaB


Mass: 81680.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)

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Photosystem I subunit ... , 2 types, 2 molecules CJ

#3: Protein Photosystem I subunit VII PsaC


Mass: 8780.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#9: Protein/peptide Photosystem I subunit IX PsaJ


Mass: 4508.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)

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Photosystem I reaction center subunit ... , 6 types, 6 molecules DEFGIK

#4: Protein Photosystem I reaction center subunit II PsaD


Mass: 16034.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#5: Protein Photosystem I reaction center subunit IV PsaE


Mass: 6850.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#6: Protein Photosystem I reaction center subunit III PsaF


Mass: 17949.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#7: Protein Photosystem I reaction center subunit V PsaG


Mass: 9806.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#8: Protein/peptide Photosystem I reaction center subunit VIII PsaI


Mass: 4352.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#10: Protein Photosystem I reaction center subunit X psaK


Mass: 8794.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)

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Protein , 1 types, 1 molecules L

#11: Protein Photosystem I reaction centre subunit XI PsaL


Mass: 12735.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)

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Light-harvesting protein of photosystem I ... , 9 types, 10 molecules 1Z37845692

#12: Protein Light-harvesting protein of photosystem I Lhca1


Mass: 20671.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#13: Protein Light-harvesting protein of photosystem I Lhca3


Mass: 23971.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#14: Protein Light-harvesting protein of photosystem I Lhca7


Mass: 24091.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#15: Protein Light-harvesting protein of photosystem I Lhca8


Mass: 22796.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#16: Protein Light-harvesting protein of photosystem I Lhca4


Mass: 22609.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#17: Protein Light-harvesting protein of photosystem I Lhca5


Mass: 24988.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#18: Protein Light-harvesting protein of photosystem I Lhca6


Mass: 24911.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#19: Protein Light-harvesting protein of photosystem I Lhca9


Mass: 20119.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coelastrella (plant)
#20: Protein Light-harvesting protein of photosystem I Lhca2 partial


Mass: 7528.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: partial / Source: (natural) Coelastrella (plant)

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Sugars , 2 types, 8 molecules

#31: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15
#33: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 22 types, 392 molecules

#21: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 213 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#23: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C40H56
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#26: Chemical ChemComp-NKP / (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate / 18:1 LPA / oleoyl lysophosphatidic acid


Mass: 436.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41O7P
#27: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#28: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2
#29: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#30: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#32: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O
#34: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10
#35: Chemical ChemComp-T7X / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H83O13P
#36: Chemical ChemComp-C7Z / (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O2
#37: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#38: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56O2
#39: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#40: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#41: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H77O8P
#42: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37NO2
#43: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44NO7P
#44: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Coelastrella sp. Photosystem I / Type: COMPLEX / Details: Contains 11 core subunits and 10 antenna proteins / Entity ID: #1-#19 / Source: NATURAL
Molecular weightValue: 0.9 MDa / Experimental value: YES
Source (natural)Organism: Coelastrella (plant) / Cellular location: Thylakoid membrane / Organelle: Chloroplast
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Chlorophyll concentration was provided
Specimen supportDetails: Harrick Plasma cleaner PDC-32G-2 / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1750 nm / Nominal defocus min: 150 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.38 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 31707

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2RELION3.1image acquisition
4CTFFIND4.1CTF correction
7PHENIXmodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2972135
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167160 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01352858
ELECTRON MICROSCOPYf_angle_d2.41774966
ELECTRON MICROSCOPYf_dihedral_angle_d33.24321550
ELECTRON MICROSCOPYf_chiral_restr0.1096311
ELECTRON MICROSCOPYf_plane_restr0.0139787

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